But human flesh was too frail, too paltry to hold the terrific essence that was Khosatral Khel. So he stood up in the shape and aspect of a man, but his flesh was not flesh; nor the bone, bone; nor blood, blood. He became a blasphemy against all nature, for he caused to live and think and act a basic substance that before had never known the pulse and stir of animate being.
In Haruhi Suzumiya, Kuyou Suou / Suou Kuyou (the proper order is purposefully left unknown). While the other Humanoid Interfaces are weird, Kuyou is described by the narration as simply wrong. Her ordinary movements like walking seem to defy the laws of physics in inexplicable ways, and her words and motivations are even less comprehensible than the others. Kyon is terrified to simply be in her presence.
In Soul Eater, many of the Great Old Ones take humanoid shapes but are regarded as something inhuman and spiritually beyond the realms of human comprehension. The primary example is probably Asura, the incarnation of madness, whose presence causes hallucinations and reality to go wibbly-wobbly. Lord Death is a more benign example, and Death the Kid looks and acts entirely human to the point that it is a a very bad sign when he denounces his connection to humanity (and life itself) in favour of his decidedly inhuman heritage.
Father looks like a normal middle aged man. He is in fact a living Philosopher's Stone made from hundreds of thousands of people, giving him unprecedented power. Then he reveals that his body is just a puppet, and his real body is spread all across Amestris. Then he fuses with the Gate of Truth and becomes something even worse.
Most of the Homunculi can easily pass for human, but their true forms show them to be almost as nasty as Father. Special mention goes to Pride (a colossal shadowy mass of tentacles, eyes, and teeth) and Gluttony (a "fake" Gate of Truth).
In Apocalypse no Toride (Fortress of The Apocalypse) the four juvenile delinquents escape from prison (which has been overrun with zombies) into the city and encounter a giant mountain of rotting zombies controlled by an androgynous naked man on the top, using the zombies like a grotesque throne. When Maeda catches its attention, said naked man (who was about a half-mile away) uses the zombies to move like a hideous organism at lightning speed, until it's only a foot in front of the terrified youth. A close-up reveals that it has Sharingan-like eyes, with three smaller eyes inhabiting each of its pupils.
Neon Genesis Evangelion has Rei and Kaworu, who are the soul (or part of a soul) of an Angel jammed into a soulless clone body, and are even more powerful and just as incomprehensible as the "regular" Angels.
Baccano! has Ronnie Schiatto, an ancient and incomprehensibly powerful "demon" who decided to take human form and become a gangster for the lulz. While he's usually content to just sit back and be the All-Powerful Bystander, sometimes he likes to switch his Lovecraftian terror aura on while still in human form - it does wonders for negotiations.
If he had just been a simple mafioso, those gathered there would not have felt such an alien sense of awe. The aura rolling off of him was that of innumerable things mixed chaotically together... of something that was not human.
Gessho Kuki, aka The Shadow, and Big Bad of Kagerou-Nostalgia may look like a man (albeit one who is deep into the Uncanny Valley) but is not, and never was, human. He's eventually revealed as a mass of evil magic left behind by previous Big Bad King Haku, and trapped in the form of a man. When he loses his temper he goes One-Winged Angel, changing into a billowing mass of magic that keeps only his human form's eyes.
Claymore has AwakenedPriscilla, a nightmare that makes other nightmares crap their pants and required a different Abomination to perform a Fusion Dance to temporarily seal her away, yet most of the time either looks like a human woman or a humanoid creature with jagged wings and a single horn. Her power so vastly outclasses the other Awakened Beings that she has been called a Physical God, but she is disinterested with the conflict between the Claymores and the Organization, her primary motivations being eating everything she comes across and hunting down Clare.
In Hellsing, Alucard looks like just an "ordinary" vampire. It turns out he's actually something far, far more horrific, being at the very least a Hive Mind of millions of undead souls, all slaved to a single once-human mind. He freely shifts through the most horrific forms at will, with his "true form" being essentially a city-swallowing ocean of blood with wailing human and animal corpses rising half-formed from its depths and potentially becoming an independent army. In the finale he goes even further, killing off his undead army to become a walking, talking quantum anomaly.
Naruto has Kaguya Ōtsutsuki, the mother of the legendary Sage of Six Paths. Where she came from and whether she was human to begin with is unknown, but she had horns, the Byakugan, a Third Eye combining the Rinnegan and Sharingan, and more chakra than the Ten-Tails itself. When she was alive she was both worshipped as a goddess and feared as a demon, and her means of bringing "peace" to the world involved using the Infinite Tsukuyomi on people and then turning them into Zetsus. When she saw her sons had inherited her power and were teaching others to use it, she transformed into said Eldritch Abomination to get it back.
In Sailor Moon, the final form of Chaos that destroys the galaxy in the far future...is a Senshi: Sailor Chaos.
Doctor Manhattan of Watchmen fame shows signs of becoming this throughout the story due to his growing detachment from, well, everything. He ultimately embraces humanity, sort of, but not his own. At best you could say he recognizes the value of humanity. What he actually does is to go off to a galaxy far, far away to play God.
The Shade looks and acts human enough (though some artists do portray him with a certain pallor), but his powers are taken straight from the fabric of a dimension holding a godlike Eldritch Abomination and have essentially become one with him, making him ageless and virtually unkillable, not to mention terrifyingly powerful. Thankfully for us, he's generally a fairly nice guy (not a hero by any means, but definitely not an outright villain either) and is perfectly willing to leave you be... that is, unless you attempt to attack Opal City. In that case, all bets are off.
Golden Age public domain superhero Stardust The Super Wizard is an unintentional one. Imagine a character with the reality-warping power of Dr. Manhattan as mentioned above combined with the black and white worldview and the "creative" mind of his "colleague" Rorschach and you have Stardust.
Mad Jim Jaspers of Captain Britain crosses into this realm thanks to his abilities being strong enough to make him nigh-omnipotent, with it being heavily implied that he exists partially in a metaphysical realm, as well. He's so powerful that his entire continuity had to be destroyed to prevent it from becoming infectious and warping reality in other continuities. Earth-616 also has Jaspers, and he's even more powerful. It took an invincible, infinitely adaptable killing machine that the original Jaspers created and that escaped from the destroyed continuity to bring the 616 Jaspers down. It transported him to a reality-free area to deprive him of fuel for his abilities. The resulting toll on the being was so great that he was put down without much difficulty by Captain UK.
Abraxas looks like a human with green skin who wears a toga, and he makes Galactus seem positively cuddly in comparison. Indeed, one of the reasons Galactus even exists is to keep Abraxas in check. Abraxas is the opposite of Eternity, making Abraxas the ultimate embodiment of unfettered destruction in the Marvel multiverse. Abraxas is fully willing and capable of killing entire universes, and the only way to get rid of him other than by reviving Galactus is to destroy all reality.
Several of the enemies of Doctor Strange, the most notable ones being Dread Dormammu, who looks like a humanoid with constantly burning head, and his sister, Umar the Unrelenting, who looks like a beautiful human woman. They are actually Faltine, a race of pure energy beings, and have power to rival Abstracts. Umar's daughter, Clea, is half-Faltine, yet looks like a human woman, only with unusually white hair. Strange also faces various gods, like Cthon (who looks like a hideous old man) and Demon Lords and Archdevils, like Mephisto (who looks like a human with unnaturally red skin).
Psyko, the warped Evil Counterpart to Sleepwalker, was originally human before he was exposed to a wave of perverted demonic energy from the Mindscape. It completely fried the brains of every other human in the area, but he simply absorbed it and turned into a humanoid... thing with bone-white skin, a skull-like face, bone-like spikes growing out of his body, insane glowing eyes, and teeth as long as a man's finger.
Yuuka Kazami in the Touhou fanfiction Imperfect Metamorphosis is horrifically powerful, inspires petrifying dread by her very presence, not even Yukari knows what the hell she is (and notes that her powers are disturbingly ineffective against her), and even with the Shadow Youkai running around and causing a mess of everything nearly everyone treats her as the bigger threat. Later events reveal she's actually an Outer God, straight out of Lovecraft.
Naruto/Sunny in Dancing With Demons is either this or past the Bishounen Line depending on who's dealing with him. Most women and many children find his hair ornaments, flawless skin, and blonde hair "beautiful". Most ninja find his red eyes, unnatural stillness, and carnivorous diet (humans if he can manage it) highly disturbing.
Played with relentlessly in Only Human, a Star Trek: The Next Generation AU where Q never regained his powers in "Deja Qu". Q makes a poor human and it becomes clear that Q's powers were simply advanced technology and his reasoning is comprehensible by humans if they know where he's coming from. Except Q is still an alien in human form and his prior existence is still so alien it is only expressible by analogy. His expectations and reactions don't make sense without that history.
Whilst already strange to pony eyes, the human in Millennium has clearly stepped beyond the point of actual humanity, being a nightmarish force instead.
The "Mystery Man" in Lost Highway, while his true morals or intention is open to interpretation, can certainly come off as this to a first time viewer. The extensive make-up that covers his eyebrows and makes him inhumanly pale and the camera's tendency to get uncomfortably close to his face during his scenes certainly doesn't help.
From the Phantasm franchise, The Tall Man is perhaps one of the best known examples of this on film. He looks like an old man in a suit, albeit an intimidating one, but is really implied to be some horrible otherdimensional conciousness wearing the form of a man named Jebadaiah Morningstar like a meat suit. He bleeds a yellowish fluid when injured and his fingers have been known to turn into hideous bug-things when severed. He is hideously strong, controls an army of deadly silver spheres, and even has some Reality Warper powers. He has a nasty agenda that involves killing people and turning them into twisted dwarfish slaves to use in another dimension.
Satan in motion pictures will often take the form of a man (or, more rarely, a woman), only to eventually reveal himself as something either grotesque or freakishly primeval.
Dr. Pretorius in Stuart Gordon's From Beyond. It's pretty clear when we see him after his first "death" that the only things still remotely human about him are his sexual deviancy and his face.
While most of the Darklords of Helgedad in Lone Wolf have humanoid proportions, Darklord Haakon is the best example. The Legends of Lone Wolf novel Claws of Helgedad reveals that Haakon has the face of a young human man. He also has unnaturally long skinny fingers and a powerfully muscled physique. A physique that is very easy to see since he has translucent skin from the neck down. Despite the physical similarities to humans, Haakon is an embodiment of pure evil just like the other Darklords.
"Everyone who saw her at the police court said she was at once the most beautiful woman and the most repulsive they had ever set eyes on. I have spoken to a man who saw her, and I assure you he positively shuddered as he tried to describe the woman, but he couldn't tell why."
Thousands of years before the classic saga, there was the Sith Emperor, introduced in Revan and the Big Bad of Star Wars: The Old Republic. He attained immortality through a ritual that drained life essences on an even larger scale than Palpatine later pulled off, draining every last bit of life on an entire planet to the point that The Force itself ceased to exist within the planet's atmosphere. Though his body's shape was still humanoid afterward, nothing else about him was. Even other Sith Lords, who by their nature see no problem with mass murder, were horrified when they learned about how he became immortal. And his intention was to go even further, because his immortality wasn't perfect enough. He was immune to natural death, but could still theoretically be killed by violence. So his plan was to create a larger-scale version of the original ritual that would drain the life of everything in the universe, which would have effectively resulted in him becoming the Force.
Fate of the Jedi has Abeloth, a former human woman who more than a hundred thousand years before the movies ended up on a planet occupied by the immortal Ones, the Father, the Son, and the Daughter. She became the Servant, but was then accepted as the Mother because she was able to control the rivalry between the Son, who represented the Dark Side, and the Daughter, who represented the Light Side. She was still mortal though, and as she aged her ability to control the Son and Daughter's rivalry diminished and she feared the loss of her family, so she tried to obtain immortality by drinking from the Font of Power as the son had and bathing in the Pool of Knowledge as the daughter had. She achieved her goal of near-immortality, but because she was a mortal and not a divine being like the ones, her body and mind became twisted beyond recognition. The Father built the Maw Installation to imprison the Mother on that planet, and she was soon became the Dark Side entity known as Abeloth. She possessed Dark Side abilities that no others possessed, inflicting paranoia on Force-sensitives and drawing them to her, who would drain then their life energy and consume them. She would then create avatars of them, which she would use to disguise herself and hide her true hideous appearance.
In The Light Fantastic, everyone expects the Things From The Dungeon Dimensions to come storming into our reality with tentacles waving, but all they need is one mind. And when Rincewind looks into Trymon's eyes, it's every bit as horrific as anything involving tentacles and Alien Geometries.
I Shall Wear Midnight introduces the Cunning Man, the shade of a fanatic witch-hunter who was so obsessed he went on even after eventually having no body. He appears as a man in black with empty holes for eyes (no, not empty eye sockets, HOLES, you can see through them) and Invisible to Normals; to those who can perceive it, he also appears to exude a terrible stench, though rather than an actual physical stench this is their mind's perception of the corruption in his. He can use mirrors, pictures and the like to enter the world, and can possess the bodies of others. To hammer home how utterly wrong he is, it should be noted that, in Discworld, the eyes always show a person's true nature. Even the gods can change anything about their appearance except their eyes. Now the Cunning Man has nothing there, as in seeing into the front and out the back of his head.
Randall Flagg, especially in The Stand, and to a lesser extent in the other books where he is the Big Bad or The Dragon. In The Stand one character claims that Flagg is actually Legion, the Biblical demon horde that Jesus cast into a herd of pigs, and Flagg claims to be Nyarlathotep himself.
The Crimson King ends up looking almost like a human too when he's finally encountered in the end. Well, it's no worse a form than the big fish.
The Beast, AKA Martin Chatwin from The Magicians is mistaken for an Eldritch Abomination at first, but during the climactic battle, his Evil Gloating reveals that, as a boy, he escaped into the fringes of the Fillory world and accepted the darker magic of its inhabitants wholeheartedly, transforming him into a god-level power. The result is not pretty◊
The Clockmaker, from Alastair Reynolds' The Prefect. Can assume any shape, but its default form resembles a stretched out human form, spindly and quicksilver. Enjoys wanton slaughter and leaving intricately designed clocks and trinkets around... which may or may not be Body Horror-inducing booby traps.
Angleton, AKA the Eater of Souls in Charles Stross' The Laundry Series is eventually revealed to be this. Subverted in that he's undeniably one of the good guys, even if he lives in the Uncanny Valley and therefore frightens the hell out of his subordinates. What happened was that he was summoned and bound in the 1930s, taught to pass for human, and eventually Humanity Ensues. Strangely, it's implied that he believes in decency and fairness more than the people around him—he's not averse to pulling a few strings for Bob and Mo's sake.
All over the place in The Dresden Files. There's the two Faerie Queens, Mab and Titania, who are unfathomable even by fae standards and the Lords of the Outer Night in the Red Court. Then there are the Faerie "mothers", who are an order of magnitude more powerful than the queens. Some Outsiders can also take humanoid form, such as "Sharkface" in Cold Days.
Comparatively minor examples, the Myrddraal are born among the Trollocs, a throwback to the Trollocs' human heritage, but warped by the Black Magic that created them. They resemble eerily pale, graceful humans except that they have smooth skin where eyes should be and have a number of bizarre abilities that cannot be explained by the series' main magic system. They're also absolutely devoid of emotion except for cold-blooded sadism and are all completely identical in terms of appearance and personality. Even human villains who encounter them are prone to remark on how unnatural they are.
Shaidar Haran, a Myrddraal that acts as the Dark One's avatar, and later an incubator of sorts.
Padan Fain, who starts out as human, but through a convoluted series of misfortunes, becomes the living embodiment of another evil power, possibly as bad as the Dark One.
"I suppose you could call them men, yes. Two legs, two arms, a head each."
The Endlords from Sword of Shadows look like tall humans in dark armor, but it's made quite plain that they are in fact cosmic forces of destruction which have been compressed into this shape, and are utterly inimical to life as we know it.
In Those That Wake, Man in Suit is a humanoid man in a suit who's so blank his features are impossible to describe, and his influence can cause you to kill yourself or try to kill those around you. This is because he's the living idea of hopelessness.
In Blood Meridian the Judge is implied to be more than he seems, but exactly what is something Man Was Not Meant To Know. He never sleeps, he never ages, he proclaims war itself to be God, he wants nothing less than absolute power over the Earth and all life upon it, and upon finding him waiting for them in the desert, every member of the Glanton gang believes they have met him before.
Anthony Fremont in It's a Good Life. While his appearance isn't fully described, he has Purple Eyes, is sometimes described as a goblin, has an "odd shadow," and was strange-looking enough that the obstetrician who delivered him freaked out and tried to kill him. There's also the matter of his Reality Warper abilities, which allow him to do essentially anything he likes. Despite this, his mind is the same as that of any other three-year-old. That's hardly any comfort to the residents of his home town of Peaksville, who are forced to pretend that everything is good lest they be turned into something horrible and sent to the cornfield.
The Others of A Song of Ice and Fire have distinct shades of this going on. Although... it's a bit hard to tell what their deal actually is, as they can also cross into The Fair Folk, An Ice Person and Necromancer territories depending on what angle you're looking at them from. Their looks are humanoid, but you'd never mistake them for human, except from a distance. Now, try to get some sleep.
The Children of the Forest might be more benign (we think) and the classically small-style elfin to look at, especially given their links with trees and the natural world. But, they're as much like The Fair Folk as the Others are... if less... overtly Dark Powers-y. Given their link to possible blood-sacrifice in the past and their decidedly non-human points of view and, well... Don't get too comfy.
Illyria's original form was a massive tentacled creature; she's an Old One, a shout-out to the Cthulhu Mythos. But since she's stolen Winifred Burkle's body, we mostly see her looking like a blue version of her.
Jasmine. The most we could get from her true form was a shadowed mass of tentacles, and she's mentioned by her abandoned demon followers as the "Blessed Devourer." Those who are immune to her mind-control charms don't see her as a beautiful woman but a corpse filled with maggots, and her true name cannot be pronounced by human words (Angel needed a stitched up demon follower because it was the only thing capable of saying her name and breaking the spell).
Buffy the Vampire Slayer had one of these as its Season Five Big Bad. Glorificus, aka Glory, was an exiled hellgod that was reduced to using a hapless human host as a timeshare. Whenever Glory takes control of its (male) host, it looks like a glamorous woman. Even in this form Glory is a Nigh Invulnerablesuperstrong menace that can rob people of their sanity and eat it.
The Time Lords at the end of the Second War in Heaven and the Last Great Time War have continued to regenerate into forms that are ideal for waging chronological war - in the first case, war against what can only be approximately described as a sapient timeline. Guess what this implies for ordinary Time Lords?
"The Pandorica Opens" has the thing the Pandorica was designed to hold: "A nameless, terrible thing, soaked in the blood of a billion galaxies. The most feared being in all the cosmos. And nothing could stop it, or hold it, or reason with it. One day it would just drop out of the sky and tear down your world." It's the Doctor.
The Celestial Toymaker, in the original series serial of the same name, resembles a middle-aged white man dressed in Mandarin robes who engages in silly, over-sized versions of board games and toys. He however controls his own universe and has vast powers over time and space. In one Expanded Universe novel, he is depicted more horribly and is outright stated to be using the powers of the Great Old Ones.
Also in the Expanded Universe, humanoid TARDISes... it's mentioned as being especially creepy when they open to take on passengers.
The Moment is one of the more understated ones and yet probably the most powerful in the series. Never mind that it's a piece of mechanics complex enough to develop a consciousness, throughout its only appearance it repeatedly and calmly punches holes in the Time Lock around the Time War. This is the same barrier that's strong enough to (mostly) seamlessly contain the full might of the Daleks, Time Lords, and every other Eldritch Abomination they brought with them. For most of its appearance it takes the form of Rose Tyler. "No, hang on... Bad Wolf".
Bad Wolf herself. After absorbing the heart of the TARDIS in "The Parting of the Ways" Rose saw everything, in all possible timelines, and possessed enough power to disintegrate an entire Dalek fleet with a thought. However it only lasted a few minutes, human bodies not capable of containing that amount of power, and the Doctor had to perform another Heroic Sacrifice to save her.
The Fendahl in "Image of the Fendahl" is an ageless deathless Hive Mind that seeks to absorb all Life Energy in the universe, and is so terrifying even looking upon it causes its victims to be rendered immobile with fear. The Fendahl Core appears as a gold-skinned human woman.
Sutekh, Fenric, the Beast, the creature on Midnight, and the Great Intelligence all manifested in human bodies (stolen human bodies) during their appearances. The Eternals also manifested in human bodies, but not in stolen ones.
BOB from Twin Peaks is this—Humanoid on the outside, Abomination within.
LOST gives us the Man in Black, a post-human entity who takes the appearance of deceased individuals when not being a cloud of black smoke.
Angels' celestial forms are completely incomprehensible to humans, and variously described as "multi-dimensional wavelengths of celestial intent" and the size of the Chrysler building. Whenever they appear in their true forms, all that is seen is a blinding light that engulfs the entire area, a booming deafening sound that are apparently their voices, everything in the vicinity getting destroyed due to their awesome presence, and are so much of a Brown Note that any humans nearby have their eyes burn out of their sockets and die. To manifest on Earth they use human vessels, which are purely intended as A Form You Are Comfortable With.
The Leviathan's of Season 7, and a bit of Season 8 are called "The Old Ones", Primordial Creatures from the Sea that became able to possess other creatures and survive on the land. Leviathans pre-date the creation of Humans, Angels, and even the Soul itself. They also pre-date any being with a soul, such as almost all forms of Monsters, including Demons. The only being said to pre-date or to have come into creation along side of them is Death himself. They were so powerful that God sealed them away in Purgatory, because he felt they threatened to consume the whole of creation. Ironically, according to Supernatural it was a benevolent Leviathan (rare as that is) who inspired the stories of H.P Lovecraft.
In Luca Turilli's Prophet of the Last Eclipse this seems to be the case with those touched by the Black Portal. They appear perfectly human, but demons (which can literally never die and may very well be true abominations in their own right) are instinctively terrified of them. And spilling the blood of one can result in The End of the World as We Know It.
Imaginos, the central figure of the Blue Oyster Cult album of the same name, is most definitely this. Admittedly, prior to being 'recruited' by Les Invisibles he was more 'humanoid' since he apparently thought of himself as human despite being a psychic shapeshifter, but afterwards he became more of a 'abomination' and is downright gleeful about it.
Marilyn Manson's concept album Antichrist Superstar has, well, the Antichrist Superstar, the reality-destroying result of The Worm becoming fed up with his sycophantic followers. While his appearance was unknown, the finished-but-unreleased video for Antichrist Superstar was leaked almost a decade later, which does show him in this form. If the Grim Reaper had sex with a fallen angel and they somehow had a kid, it would be an apt description.
Mythology and Religion
If you look at urban myth, The Grinning Man, the Moth Man, Springheeled Jack, the Cornish Owlman, La Llorona, Black-Eyed Kids, heck, quite a lot of urban myths or cryptid sightings run on this trope. Many of these things might actually result from encounters with owls, specially barn owls, which they frequently resemble with the massive eyes and wing-like arms. Owls themselves, much like some other birds, do look vaguely humanoid, being erect bipeds, which is part of why they're frequently considered unnerving.
Nyx, personification of Night from Classical Mythology. Usually represented as a beautiful female human, yet a quick look at her children - most of which she gave birth to by herself alone - should tell you what kind of being she really is. If that doesn't convince you yet, the fact that even Zeusfears her should.
Cú Chulainn, the young hero of the Ulster Cycle of Celtic Mythology, particularly of the Táin Bó Cúailnge. Though he is portrayed as being as Bishōnen as a teenaged Irish ginger can be, he is a descendant of either the Tuatha Dé Danann Lugh or the Fomorians, a monstrous race from the mythic prehistory era of Ireland. Though he is heroic and stalwart, and generally perceived as a good guy, his defining mystical characteristic is his ability to transform into various disfigured superpowered abominations through the use of his warp-spasm. After he transforms, he becomes a berserker that slaughters anything in his path, friend and foe alike. Even out of his warp spasm, he is described in the Táin as having Multicolored Hair, four multicolored dimples in each cheek, seven pupils in each eye, and seven clawed fingers and toes on each hand/foot.
Some of the angels in Abrahamic religions, such as Christianity and Judaism. It is clear that some angels like Gabriel can appear as humanoid, but their real forms are at best highly confusing and at worst mind-numbingly horrifying. And they're not even alive anyway, as their entry on Eldritch Abomination shows. Note that only some bother to appear as humanoid however, as many in The Bible and The Qur'an don't even bother to disguise their real forms.
Daniel saw an angel that was invisible to everyone else, carried with it an aura of fear, and had a glowing face (like lightning) and eyes of flame. Also a body carved from gemstones.
According to one interpretation, a lot of the angels mentioned early on in the Bible (especially in B'reshit/Genesis) are in essence the will of God made manifest in temporary human form. So while they're described as men in the text, they really really aren't.
Satan is described as "appearing in the guise of a young man."
The angel of the Lord itself is described as a man who was "terrifying to look at" by Samson's mother and when Samson's father asked its name he replied "You wouldn't understand if I told you." Despite or perhaps because of this, apocryphal works call him Metatron which basically means "less than four the letter word" (Tetragrammaton, a title for God).
Most if not all examples of The Fair Folk. To be expected, since "eldritch" originally meant "elven".
Atropals from Epic-level DnD, the stillborn fetuses of Gods, also capable of shedding smaller Atropal Scions. Unsurprisingly, they are as terrifying, powerful and hideous as the description suggests.
Daelkyr from Eberron, high-level outsiders from the plane of madness. Notable in that they looked like this when they invaded the main continent ages prior, before humans had ever set foot there. When human explorers did arrive, later, they created a panic among the demihuman populace due to the resemblance. Keith Baker, creator of Eberron, was once asked why daelkyr looked so much like humans. His response was that the real question is why do humans look so much like daelkyr...
The Lady of Pain from the Planescape setting. Beyond her vaguely humanoid appearance (a ten foot floating humanoid in a robe with no visible feet and a frozen female face surrounded by a crown of blades), nobody knows anything about what or who she is, save that anyone who disrupts Sigil's day-to-day life or directly interacts with her in any way tend to get Flayed Alive on the spot. Inside of Sigil she is essentially omnipotent and not even gods can set foot there if she doesn't want them there.
Mage: The Awakening has "the Other," the Astral Aeon of the Abyss, who is said to look simply like an unassuming, shrunken, slightly odd old man, who nevertheless has something indescribably off with everything about him.
Similarly, each of the True Fae from Changeling: The Lost has a humanoid Mask that they can wear when they appear on Earth. These masks can be beautiful or hideous, but usually within the realm of human expectation... except for the one element that's just wrong.
Even Changelings can get in on the action; when their Wyrd stat (basic supernatural power) hits 6, they manifest a certain... oddity in their Mask, which humans rationalise away but are still capable of seeing. Of course, the latter may become the former, given enough Wyrd and not enough Clarity. Turning humans into changelings is how the True Fae reproduce. Have fun with your Doomed Protagonist.
This is also what most mages think of geniuses — that they are bizarre cosmic intelligences of unknown motivation and origins who simply look human. In the case of the Illuminated, they may well be right. The "inverted Geniuses" known as Clockstoppers may also be examples — one of the most powerful is described as being more a force of nature than a man.
The Old World of Darkness has the Onceborn of Wraith The Oblivion, effectively dead gods in service of the necrotic force known as Oblivion. Unlike their cohorts, the Neverborn, they were human at one point... but they were such bastards in life, they plummeted right into becoming Spectres upon death, and then ascended to the ranks of horrible divinity.
The Yozis and their varioussouls can appear in any number of bizarre, logic-defying forms, including entire living worlds... or they can appear as inhumanly attractive humanoid beings with a few thematic characteristics here and there. They can also do both at the same time — all demons above the First Circle have the ability to manifest in multiple locations at once. The Primordials Gaia and Autochthon are just as eldritch, except they haven't been mutilated and imprisoned in Hell. Gaia's most familiar form is a beautiful humanoid goddess who hangs out in Heaven.
The Fair Folk qualify, being even more monstrous and alien in this setting than is standard for that trope — they come from what is essentially an alien universe characterized by having no laws of physics, they have no actual personalities or motives, and they can only exist in Creation by eating human souls. Yet, as far as appearance goes, many of the Raksha nobles are inhuman only in their extreme beauty. It helps attract prey, you see.
According to Word of Sol, the Green Sun Princes qualify to a degree, having taken the Yozi nature into their once-human souls, and are gradually evolving into Yozi-like beings.
In a way, all of the Exalted are this. Human beings were never meant to receive power in the manner of the Exalted, and elder Exalts tend to have viewpoints that are rather skewed for one reason or another. They can also easily be impossibly beautiful.
The Immortal God Emperor of Mankind. Long ago, all of Earth's mages, psykers, and mystics decided that humanity needed a champion to lead them. They committed mass suicide and all of them were reincarnated as one being: the Emperor. Anyone who had the misfortune to make psychic contact with him and got a glimpse of what lay beneath the surface, such as John Grammaticus (a powerful psyker in his own right), would be left in a state of total awe and terror — mostly terror. After he was put on life support he spent ten thousand years receiving worship from untold quadrillions of humans across the galaxy — in a setting strongly influenced by Clap Your Hands If You Believe.
Horus became one of these at the end of the Horus Heresy, with all four of the Chaos gods using him as a vessel of their power at once. The battle between him and the Emperor left him dead and the Emperor mortally wounded.
Over in Chuubo's Marvelous Wish-Granting Engine, there's the Best Friend and Billy Sovereign, who have ties to the Actuals of Nobilis. Billy is a pure example, but the Best Friend has actually gained a soul, which the Actuals are usually incapable of doing. Chuubo's also has Excrucians, under the name Riders, but they don't have as much world-ending horrible doom power, and all of them are at least to a degree playable out of the corebook.
Magic: The Gathering: While most pre-Mending planeswalkers were at the very least potential recruits, the post-Mending setting has given us Ashiok, Nightmare Weaver - a planeswalker who is gradually transcending humanity and becoming something else. The fact that the top of...its head is in fact black fog is what we call a "warning sign" in these parts.
Agonistes from the Tortured Souls line, who appears as a tall, powerfully-built man dressed in black leather and chains, his face horribly scarred and mutilated into a permanent Slasher Smile (if that sounds familiar, it should - the toy line was created by Clive Barker). Hand-made by an insane God on the seventh day of Creation, he answers the prayers of those who seek revenge on their enemies, remaking their bodies and transforming them into living weapons. While he isn't malicious (he only transforms people who come to him willingly), he's still beyond human morality - all he cares about is the "art" he can create with his supplicants.
Most Final FantasyBig Bads pass through this at some stage of their life cycle. They almost all pass out of it later when powering up, advancing to more conventional abominations, of course, but the intermediate stages still qualify.
Exdeath is actually an aggregate of evil souls trapped in a tree, but spends most of the game as a humanoid suit of armor. How he managed to fit a classic Eldritch Abomination appearance like his into a suit of armor small and human enough to deceive people isn't known, but he isa wizard.
Ultimecia managed to destroy time itself but still exists quite comfortably and is a Sorceress, something not quite human but looking the same, until the final boss fight; she loses the "humanoid" part when she shifts from "break the universe" mode into "break the skulls of the impudent mortals before me" mode.
Yu Yevon was once human, but turned into a jellyfish-summon-disease-thing using the only powers available to him as a human and instead simply wears an actual Eldritch Abomination as a suit of armour. He counted back in the day when he made the first Sin, though, and might have counted longer depending. We don't really know the how or why of his current blobby appearance, so it might have been a gradual thing.
Yunalesca, appearing as an attractive woman in impractical clothes until the real fight begins, yet simultaneously being an Unsent who has gone on that way a lot longer than any of the fiends you encounter under normal conditions.
Vayne Solidor started out as an ordinary Hume, albeit one who knew kung fu. Then the godlike Occuria Venat, out of gratitude for Vayne's help in fulfilling her Evil Plan, merged with him so that he would not face death alone. This fusion became The Undying, a humanoid monstrosity with pieces of Vayne's sky fortress attached to it that gave it the appearance of a mecha-angel.
Organization XIII from Kingdom Hearts II. Like the rest of their Nobody brethren, their semi-existence is so unnatural, so deeply wrong that even the darkness rejects them. Unlike the others, however, they look exactly like humans with odd powers, but in reality are just stretchy rag dolls. Mention is made that the ranked Organization members could be "demoted" to regular Nobodies. And oddly enough, being a Nobody is only a temporary affliction. Who knew that souls can regenerate?
The regular Nobodies, the aforementioned "stretchy rag dolls", have a sufficiently humanoid appearance to warrant this trope as well.
Then there's Xion, who is an honorary member of Organization XIII despite actually being a Replica, not a Nobody.
The prequel has Vanitas, a being made from another character's Darkness and is the original Unversed and origin of every Unversed you fight in the game.
Persona has Nyarlatothep taking the form of Jun's father in Innocent Sin, and of Tatsuya himself in Eternal Punishment.
In Persona 3, the Death Arcana itself is revealed to have somewhat unwittingly taken on a human form: firstly the Creepy Child Pharos, who then transforms himself and unknowingly becomes your new classmate Ryoji Mochizuki.
In the Shin Megami Tensei series, Alice, the recurring Elegant Gothic Lolita, who looks so human she has been often mistaken for an innocent, normal girl. She's actually something far worse than the series' standard Fiends and Undead. In Devil Survivor 2, her Racial Skill is Unearthly Form.
ADOM has several. Certainly there's Nuurag-Vaarn, the Chaos Archmage, who is the penultimate Boss Fight for the normal ending. He appears as a withered old man whose eyes are holes radiating such unbearable light of power you can barely catch a glimpse of the tentacles writhing in them. (Well, actually he appears as a "@" but this is what the description says.)
Heretic: Aside from the fact that we never see his face, or body for that matter, there's nothing visibly inhuman about D'Sparil's appearance, even though he's a demon that slipped in through a hole in the walls of the cosmos from the outside. He makes up for this by riding a humanoid serpent with an appropriately eldritch appearance.
The Heresiarch from Hexen, a near-unique boss creature, is an immensely powerful magic-using humanoid creature of some sort. Most of its appearance is hidden inside its robes, like D'Sparil's, but claws and a tail can be seen at the bottom. It's a leader of the cult of the Serpent Riders, but there isn't really much of an indication what it actually is, aside from something eldritch and unnatural.
Lavos from Chrono Trigger. At its core, beyond all its protective layers, it resembles nothing more than a (comparatively) small humanoid alien astronaut. That is also its most hideously powerful form, whose mere presence distorts time and space. And it's not even Lavos's real body anyways.
In League of Legends, we have Kassadin and Malzahar. Both have been touched by the Void, an extradimensional space where Lovecraftian creatures lurk. Both wield Void magics, but with very different goals. Whether anything human actually remains of them is debatable.
The GMan of Half-Life... Maybe. To be certain, he's dead center in the unnerving category, has scarily thorough, though unknown amounts of knowledge of the protagonist and events, and displays powers that are magnitudes beyond anything else in the series (it required the entire Vortigaunt race working together just to stall him, and even that didn't last long). And he says he reports to a higher power. There's a good reason a lot of fans compare him to Nyarlathotep.
As of Sengoku Basara 3, Oichi is, if not one outright, at least on her way to becoming one. She's been robbed of the last shred of her sanity, seeing the world through a bizarre, alien dream logic, and is simultaneously the master and puppet of the dark powers she showed in the previous game. She gets better in some of her endings.
Deadly Premonition has Forrest Kaysen, who is revealed to be a dimension-warping abomination. He certainly isn't as indestructible as the average Humanoid Abomination though, as Francis Zach Morgan is able to dismissively murder the son of a bitch with a well placed bullet to the brain.
In the sequel, there's Mr. Scratch, who exists as a spawn of the darkness and takes the form of Alan himself.
The Outer Space Beings from the Sin and Punishment series are from outside the universe as we know it, have strange and immense powers, have blood that can grant people special powers, are implied to be the source of many of the bizarre lifeforms found in the series... and can look perfectly human. The fluff reveals they can look like anything they want. And Achi, Big Bad of the first game, shapeshifts into a planet for the final boss fight.
Dishonored has the Outsider, an... entity that seems to have existed throughout the whole of recorded history - and before. You'd mistake him for a handsome young man in plain clothing were it not for his totally black eyeballs, his tendency to be wreathed in shadow, and that he seems to enjoy hovering a foot or so off the ground. His hobbies include speaking with polite bemusement about mortal affairs, entering people's dreams to inspire bizarre inventions, branding those he deems "interesting" with his mark to grant them really weird powers, being alternately worshipped as a god and vilified as a Satanic figure, and hanging out in a realm called The Void which may or may not be slowly consuming reality as its inhabitants know it. Anecdotal evidence suggests that he may be using A Form You Are Comfortable With, and he's actually a Space Whale... which in the Dishonored universe, means he's pretty Lovecraftian in his appearance (though far from Go Mad from the Revelation levels).
OFF, depending on the Alternate Ending you pick. It helps that the thing's on the very edge between this and a full-blown eldritch in appearance, and that from your perspective, it had you fooled the entire time.
Dark Samus, the main antagonist of the Metroid Prime trilogy, resembles a black, biomechanical version of Samus Aran. "She" began as the titular Metroid Prime, a Metroid mutated by prolonged exposure to Phazon and prophesied by the Chozo as the Worm. Following Metroid Prime's defeat at the hands of Samus, it merged with her Phazon Suit and came back as a twisted doppelganger bent on spreading Phazon throughout the universe and even other dimensions, and was unkillable as long as Phazon existed.
Amnesia: The Dark Descent: The Big Bad, Baron Alexander von Brennenburg, is eventually revealed to be a being from another universe that got exiled into our own. He takes a human form to fit in with our society, but as the game goes on it's clear he is something else. Looking at a portrait of him while low on sanity transforms his face into a horrific corpse-like visage, which is believed by some to be a glimpse at his true form.
Flemeth, the Witch of the Wilds from Dragon Age. It's not yet clear what she is, but she unnerves everybody. Her own daughter Morrigan eventually discovers that Flemeth is no mere demon-possessed mage or Blood Mage, but something worse. Fenris claims that he's met demons, blood mages, and abominations, but he can tell that Flemeth isn't any of those things. Even Justice, a Fade Spirit, has no idea what she is. The only thing certain about her is that she is dangerous. Very dangerous.
Kingdoms of Amalur: Reckoning: You. Fateweavers treat you like a walking Physical God and the Tuatha refer to you as an abomination. One NPC even has a freak out watching your power work, although to be fair he just watched you rip out an enemy's fate then use it as a weapon.
Alma evolves from a Stringy-Haired Ghost Girl to full-blown world-threatening reality-breaking abomination, yet keeps her somewhat human appearance.
The Creep in the third game: though humanoid, it is far more monstrous and aggressive than Alma. It eventually turns out that it is an amalgam of the worst memories Fettel, the Point Man, and Alma have of Harlan Wade, given life by Alma's psychic powers.
In Drakengard 3, the Intoners all look human and are anything but. Zero is the only Intoner who is even remotely a true human and the flower in her eye is changing her into something else. The others are all nascent Grotesquerie Queens who copied the forms of Zero's fellow adventurers when they were born.
Rithuly from Sluggy Freelance, a vaguely defined "dark god" with strong Eldritch Abomination vibes: his "true form is of a great flying Stygian dragon" but he "usually appears man-sized, either as a wispy tentacle-headed dark ghost or a charming handsome man in a white robe adorned with jewelry."
Gunnerkrigg Court: A look into her past reveals that Jones qualifies. Her existence predates life on Earth by at least a few billion years, but she has always looked the same. She has a perfect memory for every instant of her entire history, scratches diamonds, and is impenetrable to x-rays. She claims to lack emotions or imagination; though Antimony has her doubts on this matter, it might just be projection on her (and the readership's) part. Oh, and she has no idea what she is, either. MYSTERY SOLVED!
The Slender Man, pictured above. You can just about mistake him for a human being at a distance (unless he's in full-on Combat Tentacles mode), but come any closer and you start to... noticethings. Marble Hornets, one of the most famous Slendy stories, is an excellent portrayal of this trope. The Slender Man distorts reality just by existing, driving some characters into homicidal madness. He seems to have a goal of some sort, but whatever it is, it's utterly inscrutable.
Another well-known creepypasta creation, The Rake, also counts. A freakish hairless dog-man who seems to have similar stalking habits to Slenderman, albeit being more direct with his victimsnote Slendy watches from a distance; the Rake likes to sit on your bed. While you're in it. Has even showed up in Everyman HYBRID, integrating it into the above mythos.
The SCP Foundation has absolutely every type of abomination, and these are no exception. There's some serious creepyReality Warpers hanging around there.
Dr. Clef claims to be one himself: he discovered what he was at an early age when an idle thought caused the Challenger disaster. He then devoted his life to putting the kibosh on those more selfishly inclined than he. This is still Clef, though, so take it as you will...
Creepy Child SCP-053 looks and acts like an ordinary three year old girl. She's not. Let's put it this way: SCP-682, an alien reptilian Omnicidal Maniac that hates everything in this universe on principle, likes SCP-053, and the feeling is mutual — once SCP-053 got past her initial fear of the giant terrifying reptiloid. (It's kind of adorable, actually.)
SCP-106 is an entity that resembles a decomposing old man that corrodes everything it touches and has its own Pocket Dimension that it lords over.
SCP-096 is a tall skinny being with disproportionately long arms and enters an Unstoppable Rage and screams like a human when someone looks at its face, regardless of how indirect the method is, and will proceed to kill and [DATA EXPUNGED] that person leaving no trace of them.
Along the lines of the Slender Man, SCP-582 appears and acts out his part in any stories written about him.
Sara Waite, codename Carmilla. She looks like a goddess of lust. Her father's mother is actually Shub-Niggurath. Her mother's ancestry is even creepier.
Tennyo is somehow related to some Eldritch Abomination that was created to eat/destroy the Eldritch Abominations of the Cthulhu Mythos, something that would look at Cthulhu and think "ooh, an appetizer!"
Atop the Fourth Wall: The Entity/Missingno can apparently only manifest itself in the physical realm by taking the form of another.
In Worm, Scion, the world's first and greatest superhero, is the avatar of an immensely powerful and ancient alien entity.
Popo from Dragon Ball Z Abridged terrifies the protagonists, attempting to contact him psychically caused King Kai to short out, and is implied to be vastly more powerful than anyone in the series. He reveals a glimpse of his true nature as he eats Garlic Jr.
Miss Bitters from Invader Zim. Nobody is exactly sure what she is, but human is not on the list of options. She is implied to be older than the Skool (they couldn't make her move so they built it around her and made her a teacher) and has taught at least two generations worth of students. The official website mentions rumors that she is the spawn of an English teacher and a really big snake. Her flashbacks in the series indicate she was once much happier...
Wall-Mart, a "fictional" chain store in the South Park episode "Something Wall-Mart This Way Comes". Wall-Mart is actually portrayed as a complete Eldritch Abomination in the episode, being an abstract entity from beyond that exists as long as there is consumerism and poisons every town in which it manifests itself. Near the end of the episode however, it temporarily takes on human form (looking a lot like Vincent Price, oddly enough) so it can talk to Stan and Kyle. Played for laughs at the climax with the Vincent Price-thing laughing maniacally and declaring "Now you shall see me as I truly am!" - but all he does is tear off his gray mustache, then take off his white hat and wave it around wildly as the store around them collapses like a cave-in at a mine shaft.